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- PDB-4dqk: Crystal structure of the FAD binding domain of cytochrome P450 BM3 -

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Basic information

Entry
Database: PDB / ID: 4dqk
TitleCrystal structure of the FAD binding domain of cytochrome P450 BM3
ComponentsBifunctional P-450/NADPH-P450 reductase
KeywordsOXIDOREDUCTASE / Rossmann Fold / redox partner to cytochrome P450 / FAD and NADP binding / none
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol
Similarity search - Function
NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Elongation Factor Tu (Ef-tu); domain 3 ...NADPH-cytochrome p450 Reductase; Chain A, domain 3 / NADPH-cytochrome p450 Reductase; Chain A, domain 3 / Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Up-down Bundle / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJoyce, M.G. / Leys, D.
CitationJournal: Febs J. / Year: 2012
Title: The crystal structure of the FAD/NADPH-binding domain of flavocytochrome P450 BM3.
Authors: Joyce, M.G. / Ekanem, I.S. / Roitel, O. / Dunford, A.J. / Neeli, R. / Girvan, H.M. / Baker, G.J. / Curtis, R.A. / Munro, A.W. / Leys, D.
History
DepositionFeb 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional P-450/NADPH-P450 reductase
B: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,52314
Polymers87,5992
Non-polymers2,92412
Water4,936274
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A: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2627
Polymers43,7991
Non-polymers1,4626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bifunctional P-450/NADPH-P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2627
Polymers43,7991
Non-polymers1,4626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)191.387, 191.387, 74.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Bifunctional P-450/NADPH-P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Cytochrome P450 102 / NADPH--cytochrome P450 reductase


Mass: 43799.480 Da / Num. of mol.: 2 / Fragment: Cytochrome P450 BM3,UNP residues 659-1049 / Mutation: C774A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CYP102A1, cyp102 / Production host: Escherichia coli (E. coli)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.48 Å3/Da / Density % sol: 72.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2 microL of mother liquor to 2 microL of 12 mg/ml FAD domain. Crystals were obtained using a well solution of 28% polyethylene glycol 8000, 0.3 M ammonium sulfate, cacodylate buffer pH 6.5. ...Details: 2 microL of mother liquor to 2 microL of 12 mg/ml FAD domain. Crystals were obtained using a well solution of 28% polyethylene glycol 8000, 0.3 M ammonium sulfate, cacodylate buffer pH 6.5. Crystals of dimensions 70 x 70 x 900 M formed after 4-7 days. In order to form a coenzyme complex with NADP+, C773A/C999A FAD domain crystals were soaked in a 10 mM NADP+ solution for 10 minutes., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 5, 2003
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→29.36 Å / Num. all: 57823 / Num. obs: 57823 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.36 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.804 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25647 3086 5.1 %RANDOM
Rwork0.21292 ---
all0.21507 57823 --
obs0.21507 57823 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.578 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5855 0 181 274 6310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0226158
X-RAY DIFFRACTIONr_bond_other_d0.0010.024108
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.9998362
X-RAY DIFFRACTIONr_angle_other_deg1.09310045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52824.186258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11215987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8711536
X-RAY DIFFRACTIONr_chiral_restr0.1270.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021179
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1671.53799
X-RAY DIFFRACTIONr_mcbond_other0.2661.51529
X-RAY DIFFRACTIONr_mcangle_it2.22226081
X-RAY DIFFRACTIONr_scbond_it3.42632359
X-RAY DIFFRACTIONr_scangle_it5.5134.52281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 214 -
Rwork0.421 4157 -
obs--100 %

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